Sisiphos (temporarily closed right now I believe, not sure if that'll be the case by May), Renate, Birgit, Ritter Butzke.
I don't think even Golden Gate nor ://about:blank would be considered truly "underground" anymore. As usual with the underground stuff you need to dig deeper to find them, as I don't live in Berlin I need to rely on my local friends to take me to these places as they are inserted within the underground culture.